Do novel acidophilic archaeal ammonia oxidisers solve the paradox of nitrification in acid soils?

新型嗜酸古菌氨氧化剂能否解决酸性土壤中硝化的悖论？

• 批准号: NE/I027835/1
• 负责人: Graeme Nicol
• 金额: $ 54.89万
• 依托单位: University of Aberdeen
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2011
• 资助国家: 英国
• 起止时间: 2011 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FI027835%2F1
• 关键词: Do; novel; acidophilic; archaeal; ammonia

Nitrification is an essential process in the cycling of nitrogen throughout the planet. The process consists of the conversion of ammonia to nitrate by two groups of microorganisms. Ammonia oxidisers convert ammonia to nitrite and this is then converted to nitrate by nitrite oxidisers. Although beneficial to some plants, nitrification can have deleterious consequences. Ammonium can be retained in soil but, after conversion to nitrate, it is leached from soil, polluting groundwaters that may be used to supply drinking water. It also contributes to atmospheric pollution, as ammonia oxidation is accompanied by production of nitrous oxide, a potent greenhouse gas that also contributes to destruction of stratospheric ozone. None of the ammonia oxidisers that have been grown in the laboratory can grow at low pH, but nitrification occurs in acid soils and there is actually evidence that rates are slightly greater at low pH. Approximately 30% of the world's soils are acidic (pH less than 5.5), mainly due to microbial activity, including that of nitrifiers. They represent a wide range of natural and managed habitats including forestry, agriculture and grasslands. Acid soils are therefore of great environmental and economic importance and it is important that we understand the mechanisms leading to nitrification in these soils. Several explanations have been proposed to explain ammonia oxidation at low pH, but none provides a full explanation and all are difficult to demonstrate in soil. Traditionally, the most important soil ammonia oxidisers were thought to be bacteria but we now know that the thaumarchaea, another group of abundant soil organisms, can oxidise ammonia. Thaumarchaea are a group within the archaea, a domain of microbial life distinct from the bacteria. Although they resemble bacteria in many ways, they are evolutionarily distinct and were previously thought to be restricted to 'extreme' environments. We recently obtained evidence that two groups of thaumarchaeal ammonia oxidisers are restricted to acid soils, suggesting adaptation to growth at low pH. We then obtained a culture of an organism, Nitrosotalea devanaterra, which is representative of one of the groups and showed it to be a strict, acidophilic ammonia oxidiser that grows only within the pH range 4 - 5.5. At these pH values, ammonia availability will be extremely low, because most will be ionised to ammonium. N. devanaterra must therefore possess unique mechanisms for ammonia oxidation at low pH that enable it to occupy this improbable environmental niche in acid soils. A major aim of the project will therefore be to determine the mechanism by which N. devanaterra grows at low pH. We also aim to obtain a culture of the second group of acidophilic thaumarchaeal ammonia oxidisers, identified in our earlier studies, and to determine whether both groups utilise the same mechanism. Potential mechanisms will be investigated by sequencing and analysing all of the genes in both strains and identifying which genes are expressed when they are growing at low pH. These mechanisms will then be tested in laboratory growth experiments.The second major aim is to determine whether these organisms are actually important in nitrification in acid soils. We will use soil laboratory systems (microcosms) to determine their ability to grow in a range of acid soils and determine whether their growth is associated with ammonia oxidation. We will manipulate soil pH, to determine the influence of pH on their growth and activity, and we will also determine whether the physiological mechanisms that explain growth at low pH in laboratory culture explain growth in acid soils.

硝化作用是氮在地球上循环的一个重要过程。该过程由两组微生物将氨转化为硝酸盐组成。氨氧化剂将氨转化为亚硝酸盐，然后由亚硝酸盐氧化剂转化为硝酸盐。硝化作用虽然对某些植物有益，但也会产生有害的后果。铵可以保留在土壤中，但在转化为硝酸盐后，它会从土壤中浸出，污染可能用于供应饮用水的地下水。它还造成大气污染，因为氨氧化会产生一氧化二氮，一氧化二氮是一种强有力的温室气体，也会破坏平流层臭氧。在实验室中生长的氨氧化剂都不能在低pH值下生长，但硝化作用发生在酸性土壤中，实际上有证据表明，在低pH值下硝化率略高。世界上大约30%的土壤是酸性的（pH值低于5.5），主要是由于微生物的活动，包括硝化细菌。它们代表了广泛的自然和管理栖息地，包括林业，农业和草原。因此，酸性土壤具有重要的环境和经济意义，重要的是我们要了解导致这些土壤硝化作用的机制。已经提出了几种解释来解释低pH下的氨氧化，但没有一个提供了完整的解释，所有这些都很难在土壤中证明。传统上，最重要的土壤氨氧化剂被认为是细菌，但我们现在知道，另一组丰富的土壤生物，thaumarchaea，可以氧化氨。Thaumarchaea是古细菌中的一个群体，是与细菌不同的微生物生命领域。虽然它们在许多方面与细菌相似，但它们在进化上是不同的，以前被认为仅限于“极端”环境。我们最近获得的证据表明，两组thaumarchaeal氨氧化剂仅限于酸性土壤，这表明适应生长在低pH值。然后，我们获得了一个培养的有机体，Nitrosotalea devanaterra，这是代表的一个组，并表明它是一个严格的，嗜酸性氨氧化剂，仅生长在pH值范围4 - 5.5。在这些pH值下，氨的可用性将非常低，因为大多数将被电离为铵。N.因此，devanaterra必须具有在低pH值下进行氨氧化的独特机制，使其能够在酸性土壤中占据这种不可能的环境小生境。因此，该项目的一个主要目标是确定N。devanaterra生长在低pH值。我们还旨在获得第二组嗜酸性thaumarchaeal氨氧化剂，在我们早期的研究中确定的文化，并确定是否两组利用相同的机制。通过对两种菌株中的所有基因进行测序和分析，并确定哪些基因在低pH值下生长时表达，将研究潜在的机制。然后将在实验室生长实验中测试这些机制。第二个主要目的是确定这些生物体是否在酸性土壤中的硝化作用中实际上很重要。我们将使用土壤实验室系统（缩影），以确定他们的能力，在一系列酸性土壤中生长，并确定他们的增长是否与氨氧化。我们将操纵土壤pH值，以确定pH值对它们的生长和活性的影响，我们还将确定在实验室培养中解释低pH值下生长的生理机制是否可以解释酸性土壤中的生长。

项目成果

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota.

• DOI: 10.1038/ismej.2015.101
• 发表时间: 2016-01
• 期刊: The ISME journal
• 作者: Oton EV;Quince C;Nicol GW;Prosser JI;Gubry-Rangin C
• 通讯作者: Gubry-Rangin C

Ammonia-oxidising archaea living at low pH: Insights from comparative genomics.

• DOI: 10.1111/1462-2920.13971
• 发表时间: 2017-12
• 期刊: Environmental microbiology
• 影响因子: 5.1
• 作者: Herbold CW;Lehtovirta-Morley LE;Jung MY;Jehmlich N;Hausmann B;Han P;Loy A;Pester M;Sayavedra-Soto LA;Rhee SK;Prosser JI;Nicol GW;Wagner M;Gubry-Rangin C
• 通讯作者: Gubry-Rangin C

Characterisation of terrestrial acidophilic archaeal ammonia oxidisers and their inhibition and stimulation by organic compounds.

陆地嗜酸古菌氨氧化剂的表征及其有机化合物的抑制和刺激

• DOI: 10.1111/1574-6941.12353
• 发表时间: 2014-09
• 期刊: FEMS microbiology ecology
• 影响因子: 4.2
• 作者: Lehtovirta-Morley LE;Ge C;Ross J;Yao H;Nicol GW;Prosser JI
• 通讯作者: Prosser JI

Identifying Potential Mechanisms Enabling Acidophily in the Ammonia-Oxidizing Archaeon "Candidatus Nitrosotalea devanaterra".

• DOI: 10.1128/aem.04031-15
• 发表时间: 2016-05
• 期刊: Applied and environmental microbiology
• 影响因子: 4.4
• 作者: Lehtovirta-Morley LE;Sayavedra-Soto LA;Gallois N;Schouten S;Stein LY;Prosser JI;Nicol GW
• 通讯作者: Nicol GW

Isolation of 'Candidatus Nitrosocosmicus franklandus', a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration.

• DOI: 10.1093/femsec/fiw057
• 发表时间: 2016-05
• 期刊: FEMS microbiology ecology
• 影响因子: 4.2
• 作者: Lehtovirta-Morley LE;Ross J;Hink L;Weber EB;Gubry-Rangin C;Thion C;Prosser JI;Nicol GW
• 通讯作者: Nicol GW